PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Potri.009G011800.4
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family ARF
Protein Properties Length: 716aa    MW: 79222 Da    PI: 6.6497
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.009G011800.4genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.61.1e-23153254199
                         EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                         f+k+lt sd++++g +++p++ ae++      + +++ s++l  +d++g +W++++iyr++++r++lt+GW+ Fv++++L +gD v+F   
  Potri.009G011800.4 153 FCKTLTASDTSTHGGFSVPRRAAEDCfpsldyK-QQRPSQELLAKDLHGVEWRFRHIYRGQPRRHLLTTGWSIFVSQKNLVSGDAVLFL-- 240
                         99****************************963.3445679************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         + +++el+++++r+
  Potri.009G011800.4 241 RGEGGELRLGIRRA 254
                         4499*******996 PP
2Auxin_resp25.17.5e-102963205882
          Auxin_resp  58 rlsGtvvgvsdldpvrWpnSkWrsL 82 
                         r+sG+v+g+ dldp++WpnSkWr+L
  Potri.009G011800.4 296 RCSGVVTGTADLDPYKWPNSKWRCL 320
                         679*********************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.106.4E-40143265IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.7E-43145260IPR015300DNA-binding pseudobarrel domain
CDDcd100179.21E-22151253No hitNo description
PROSITE profilePS5086312.872153255IPR003340B3 DNA binding domain
SMARTSM010194.1E-22153255IPR003340B3 DNA binding domain
PfamPF023621.2E-21153254IPR003340B3 DNA binding domain
PfamPF065071.8E-5296320IPR010525Auxin response factor
SuperFamilySSF542776.38E-10604689No hitNo description
PROSITE profilePS5174522.527610692IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
GO:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 716 aa     Download sequence    Send to blast
MEIDLNHPVT EVEKNSFCTN GDSSCSSNSS SSPVSSSIYL ELWHACAGPL TSLPKKGNVV  60
VYFPQGHLEQ LASSSPFSHR DMPNFDLHPQ IFCKVVNVQL LANRENDEVY TRLTLLPQPE  120
VVGQDLEGKE LQELGVDGEG DDASPTKSTP HMFCKTLTAS DTSTHGGFSV PRRAAEDCFP  180
SLDYKQQRPS QELLAKDLHG VEWRFRHIYR GQPRRHLLTT GWSIFVSQKN LVSGDAVLFL  240
RGEGGELRLG IRRAARPRNG LPDSVTGKQN SLPSALSLVS NAISTKSVFT VSYSPRCSGV  300
VTGTADLDPY KWPNSKWRCL MVRWDEDVIS DHQERVSPWE IDASVSLPPL IIQSSPRLKK  360
LRTGLQAAPP DKPIAGGGGF LDFKESVRSS KVLQGQENVG LLSPVYRCDT VNHPLDFEVR  420
NKAQQNLILT GIEKAKISEL TRAHPATHTG FTESDRFLKV LQGQEICSLS SVGALGKPNT  480
GRSSFQMYPG PRPAFYPVAA ESLRSMYFPY GDVYKNGQDP RTQSYAIFSR ENAHFNTSSI  540
QTCVVREEVR KPNQSSEYKT QESISAAPAL CANLRNQKDD FFNGNATGCK LFGFSLNAET  600
SPNSQNTSKR SCTKVHKQGS LVGRAIDLSR LNGYSDLLNE LERLFSMEGL LRNPEEGWRI  660
LYTDSENDVM VVGDDPWLEF CNVATKIHIY TQEEVEKMTV GITGDDTQSC LDQAL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A2e-95243422353Auxin response factor 1
4ldy_B2e-95243422353Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pth.131227e-59leaf| stem
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078}.
Functional Description ? help Back to Top
Source Description
UniProtAuxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. {ECO:0000269|PubMed:12036261}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.009G011800.4
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEF1447355e-56EF144735.1 Populus trichocarpa clone WS01117_J13 unknown mRNA.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024464633.10.0LOW QUALITY PROTEIN: auxin response factor 4
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLA0A3N7FHN90.0A0A3N7FHN9_POPTR; Auxin response factor
STRINGXP_002526369.10.0(Ricinus communis)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60450.10.0auxin response factor 4
Publications ? help Back to Top
  1. Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY
    TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors.
    Mol. Gen. Mikrobiol. Virusol., 2013.
    [PMID:24003511]
  2. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  3. Pashkovskiy PP,Kartashov AV,Zlobin IE,Pogosyan SI,Kuznetsov VV
    Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants.
    Plant Physiol. Biochem., 2016. 104: p. 146-54
    [PMID:27031426]
  4. Matsumura Y, et al.
    A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis.
    Biol Open, 2016. 5(7): p. 942-54
    [PMID:27334696]
  5. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  6. Liu Z, et al.
    ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis.
    Plant Cell Physiol., 2018. 59(1): p. 179-189
    [PMID:29145642]